bioinformatics-list September 2018

bioinformatics-list@list.utas.edu.au

1 participants
3 discussions

FW: DKD EVENT on THUR OCT 4 at IMAS: DataTas Seminar Series: Practical Machine Learning
by Michael Charleston 27 Sep '18

27 Sep '18

Machine Learning is fantastically useful: come and learn all you can about it from some local experts! This will be a great fun event. Please come along (I can’t because I’ll be on leave). Note the catered mixer afterwards... :) Cheers Mike -- Michael Charleston [cid:image001.png@01D3BAAE.D622B130] Theoretical Phylogenetics Group Organiser of Phylomania<http://www.maths.utas.edu.au/phylomania/phylomania2018.htm> conference 2018 November 21-23 Associate Professor in Bioinformatics Co-director of Data, Knowledge and Decisions University Research Theme Associate Head of School (Learning and Teaching) School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 From: Anya Reading <anya.reading(a)utas.edu.au> Date: Thursday, 27 September 2018 at 10:28 am To: Michael Charleston <michael.charleston(a)utas.edu.au> Subject: DKD EVENT on THUR OCT 4 at IMAS: DataTas Seminar Series: Practical Machine Learning View this email in your browser<https://protect-au.mimecast.com/s/MnSICwVLP8HgK8nJsVduTT?domain=mailchi.mp> [https://gallery.mailchimp.com/ed2707231cb1dfea612784f96/images/a95a3d3e-50e…] DATA TAS SEMINAR SERIES 2:00pm - 5:00pm October 4, 2018 // IMAS Waterfront Building (Aurora) Hello DataTasmanians, We're pleased to announce our next Seminar Series on Machine Learning to be held 2:00pm - 5:00pm October 4 in the Aurora Lecture Theatre, IMAS waterfront building. DataTas is partnering with the UTAS Research Theme for Data, Knowledge, Decisions (DKD) to bring you this exciting joint event. This session, we have Professor Anya Reading, the leader of the Compute Earth group (UTAS) giving us an introduction to Machine Learning and its application for research. We also have Matilda Brown (UTAS) to talk to us about Support Vector Machines (SVMs) in ecological research and Ben Schroeter (IMAS, BoM) to give us some practical tips on tuning Artificial Neural Networks (ANNs). After the session we will hold an informal gathering in the Flex Space (catered!) where you can chat with the speakers and other ML enthusiasts, and where we will discuss the formation of a Machine Learning community of practice in Hobart. See you there! DataTas [https://gallery.mailchimp.com/ed2707231cb1dfea612784f96/images/3addec25-dcd…] Learning from data: A partnership of mind and machine Anya Reading (UTAS) The presentation provides an overview and introduction to the use of Machine Learning in research. Anya will outline the main approaches to using 'the machine’ to learn from data, unsupervised and supervised learning, including the advantages and limitations of ML algorithms in current use. She will show how to gain research insight from ML outputs using examples from the Compute Earth research group, and show how the strengths of both humans and computers may be used together for best results. Anya Reading came to UTAS in 2007. She leads the Compute Earth group which pioneers geophysical data collection in remote or challenging locations such as Antarctica and outback Australia. This adventuring spirit extends to exploring and extending the ways that we can use computers to learn from data, and also to initiatives such as Art-Science data visualisation. She is Professor of Geophysics, in Physics at UTAS Sandy Bay, with strong connections to Earth Sciences and IMAS. [https://gallery.mailchimp.com/ed2707231cb1dfea612784f96/images/f5629458-855…] Support Vector Machines in Ecology Matilda Brown (UTAS) Matilda will describe some of the practical uses of machine learning – in particular, Support Vector Machines (SVMs) in ecological studies. Matilda will give us a brief introduction to SVMs, and go on to describe some of their applications in her PhD. This includes pixel classification in image analysis, environmental and taxonomic identification from the processed images, and detection of ecological changes in the fossil record. Matilda Brown is a PhD student in Biological Sciences at the University of Tasmania. She is working with Greg Jordan, Tim Brodribb and Barbara Holland to find new ways of applying Machine Learning techniques to answer palaeoecological questions. Matilda has spent most of her adult life trying to get people excited about leaves - either as a bushwalking guide, demonstrator or academic. She is interested in making life easier for other biologists and investigating the ecological and evolutionary history of our flora. [https://gallery.mailchimp.com/ed2707231cb1dfea612784f96/images/cc1c5091-450…] Tuning the Machine: Practical tips for training Artificial Neural Networks Ben Schroeter (IMAS, Bureau of Meteorology) Artificial Neural Networks (ANNs) provide a convenient way to model highly nonlinear systems. With the emergence of plug-and-play libraries (i.e. TensorFlow) they are more accessible than ever but remain to many a black box with a few dials and buttons for tuning. Through his masters research into the application of Machine Learning to rainfall estimation, Ben will share some practical tips on how to tune an ANN and offer suggestions on how to avoid some of the common pitfalls, such as overfitting and suboptimal minima. No idea what those mean? That's OK! Ben will give you a crash course and some ideas to help you tune your model. Ben Schroeter is a Support Scientist at the Bureau of Meteorology working on the next generation of city-scale Numerical Weather Prediction (NWP) models, and PhD candidate at the Institute for Marine and Antarctic Studies working on Antarctic NWP. Ben enjoys tackling challenging computer science problems and melting CPUs/GPUs with parallelised code. [https://cdn-images.mailchimp.com/icons/social-block-v2/dark-twitter-48.png]<https://protect-au.mimecast.com/s/Xv5wCMwv0mfvXOYMfqMNEa?domain=github.us15…> @datatas<https://protect-au.mimecast.com/s/HrLpCNLwPnfw7lpDI3oltw?domain=github.us15…> [https://cdn-images.mailchimp.com/icons/social-block-v2/dark-facebook-48.png]<https://protect-au.mimecast.com/s/WuVzCOMxQoFEnRkzF9omK_?domain=github.us15…> datatasau<https://protect-au.mimecast.com/s/ykfaCP7yRptJWGn8iJy4qk?domain=github.us15…> [https://cdn-images.mailchimp.com/icons/social-block-v2/dark-link-48.png]<https://protect-au.mimecast.com/s/-8ZvCQnzVqtJOALMilra93?domain=github.us15…> datatas.com<https://protect-au.mimecast.com/s/OCA0CROAWrhyEmXjuV3IcL?domain=github.us15…> [https://cdn-images.mailchimp.com/icons/social-block-v2/dark-github-48.png]<https://protect-au.mimecast.com/s/Qb5uCVAG1yhz3w8NHo58rP?domain=github.us15…> datatas<https://protect-au.mimecast.com/s/zsSsCWLJ2zfNO98RCMGiwB?domain=github.us15…> [https://cdn-images.mailchimp.com/icons/social-block-v2/dark-forwardtofriend…]<mailto:datatasau@gmail.com> Email<mailto:datatasau@gmail.com> JOIN DATATAS Become a full member of DataTas for the cost of a couple of cups of coffee and get access to exclusive member benefits. Student: $5/yr non-Student: $10/yr (Registration available at all our events) Copyright © 2018 DATA TAS, All rights reserved. You are receiving this email because you opted in at our website or provided your details to us at one of our events. Our mailing address is: DATA TAS Tasmanian University Union, PO Box 5055, University of Tasmania LPO Sandy Bay, Tas 7005 Australia Add us to your address book<https://protect-au.mimecast.com/s/UkAvCXLK3Afk25ZVTzxhHa> Want to change how you receive these emails? You can update your preferences<https://protect-au.mimecast.com/s/dqCdCJypLjFgZro3sKWIBK?domain=github.us15…> or unsubscribe from this list<https://protect-au.mimecast.com/s/pzNxCK1qMkfZOEkzFk1IQG?domain=github.us15…>. [Email Marketing Powered by MailChimp]<https://protect-au.mimecast.com/s/mDRuCL7rNltlKj2ytYZtdW?domain=mailchimp.c…> University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

1 0

Reminder of next week's Galaxy Workshop on finding genetic variants in bacterial sequence data
by Michael Charleston 07 Sep '18

07 Sep '18

[cid:image001.png@01D446BE.EF3A4150] SEP. 12 Introduction to Galaxy Australia-Variant Detection (University of Tasmania) by EMBL-ABR<https://www.eventbrite.com.au/e/introduction-to-galaxy-australia-variant-de…> DATE AND TIME Wed. 12 September 2018 1:00 pm – 4:00 pm AEST Add to Calendar<https://www.eventbrite.com.au/e/introduction-to-galaxy-australia-variant-de…> LOCATION Room 473 / Video Conference Room, Centenary Building Sandy Bay Campus University of Tasmania Hobart, TAS 7005 View Map<https://www.eventbrite.com.au/e/introduction-to-galaxy-australia-variant-de…> Hello all, Don’t forget the second of our Galaxy workshops is next week! You can still register here: https://variant-detection-galaxy-embl-abr-utas.eventbrite.com.au<https://variant-detection-galaxy-embl-abr-utas.eventbrite.com.au/> – and you really should! Here is a snapshot of the feedback from the first one that we ran all those weeks ago (not many): In total there were 94 people around Australia taking part. We had 58 responses to the evaluation survey, and to give you an idea about the feedback: - 100% of participants thought 'This was a useful workshop that enhanced my knowledge and skills.' - all except for 1 person thought 'The content reflected the learning objectives of the workshop', 'The learning from this program increased my level of skills' and 'The exercises and activities enhanced my learning'. - 100% said they agreed or strongly agreed with "The facilitator/s was/were organised and confident in the program content" and "The facilitator/s was/were responsive to individual questions and needs".... "Thanks for the local mentors!!" - participants signed off with things like: "Good workshop - will make sure other members of my team attend these in future" and "I thought it was a nice workshop that blended both hands on activities and some lecture based materials for follow up. Great job. Thanks! I hope to come to more." I hope to see you there! -- Michael Charleston [cid:image001.png@01D3BAAE.D622B130] Theoretical Phylogenetics Group Organiser of Phylomania<http://www.maths.utas.edu.au/phylomania/phylomania2018.htm> conference 2018 November 21-23 Associate Professor in Bioinformatics Co-director of Data, Knowledge and Decisions University Research Theme Associate Head of School (Learning and Teaching) School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

1 0

Fw: COMBINE18 Registrations Open! (*and not for long!)
by Michael Charleston 03 Sep '18

03 Sep '18

From: COMBINE Symposium <symposium=combine.org.au(a)mail122.sea21.rsgsv.net> on behalf of COMBINE Symposium <symposium(a)combine.org.au> Sent: Monday, August 20, 2018 8:29:59 AM To: Andrew Phipps Subject: COMBINE18 Registrations Open! COMBINE Symposium 2018-08-20 View this email in your browser<https://protect-au.mimecast.com/s/c6QnC6X1k7CM3x25fpWtZn?domain=mailchi.mp> [https://gallery.mailchimp.com/3f6e1d0b6a995d4581459ac68/images/31dca1b2-516…] <https://protect-au.mimecast.com/s/XoeACANZy7iVmMykUm5pKT?domain=combine.us9…> Dear Andrew, We would like to let you know that registrations and abstract submissions for the 2018 COMBINE Student Symposium are now open! The COMBINE Student Symposium is an annual, non-profit conference that aims to gather a diverse group of students and ECRs who are curious, passionate and eager to learn more about bioinformatics and computational biology. We also pride ourselves on providing a welcoming and friendly environment and encouraging networking and collaboration between attendees. The 2018 symposium will be held on Monday 26 November at the University of Melbourne (Parkville Campus) in conjunction with the ABACBS 2018 National Conference (27-28 November) and associated workshops and meetings. Travel scholarships are available to help people attend the COMBINE Symposium and ABACBS National Conference. To be eligible for a travel scholarship you must be a financial member of ABACBS (student membership is $20) and reside outside of Melbourne. For more details, including key dates and registration information, head over to our website: combine.org.au/symposium-2018/<https://protect-au.mimecast.com/s/AgSCCBNZz7iAZ3QYU8e3oB?domain=combine.us9…>. To keep up to date with details about the symposium consider joining our Facebook group<https://protect-au.mimecast.com/s/audbCD1jB7fM6Q24fozkVN?domain=combine.us9…> or following us at @combine_au<https://protect-au.mimecast.com/s/RwxuCE8kD7fnAKrET1h_So?domain=combine.us9…> and #COMBINE18<https://protect-au.mimecast.com/s/cwl_CGvmG7fqyoxvCjrfBM?domain=combine.us9…> on Twitter. Any help you can give us to advertise these events to our bioinformatics colleagues would be greatly appreciated! A flyer for advertising the 2018 COMBINE Symposium can be found here<https://protect-au.mimecast.com/s/k3kICJypLjFy4PGNtPLZDF?domain=combine.us9…>. We look forward to seeing you there! 2018 COMBINE Symposium committee COMBINE is an organisation for Australian students in computational biology, bioinformatics, and related fields. We are the student subcommittee of The Australian Bioinformatics And Computational Biology Society (ABACBS)<https://protect-au.mimecast.com/s/tavACK1qMkf9A0gVSq-PHe?domain=combine.us9…> as well as the official International Society for Computational Biology (ISCB)<https://protect-au.mimecast.com/s/g0VsCL7rNltXo5x6iW7Esh?domain=combine.us9…> Regional Student Group (RSG) for Australia. [Website]<https://protect-au.mimecast.com/s/3f-eCMwv0mf9oGKNSLrAwI?domain=combine.us9…> Website<https://protect-au.mimecast.com/s/ZytoCNLwPnf9n1K4S2k6ED?domain=combine.us9…> [Facebook]<https://protect-au.mimecast.com/s/5tw0COMxQoFwPoVWfG-V-A?domain=combine.us9…> Facebook<https://protect-au.mimecast.com/s/jjwxCP7yRptZDqYpi5ST_6?domain=combine.us9…> [Twitter]<https://protect-au.mimecast.com/s/BsjKCQnzVqt9DmG0Smm8mL?domain=combine.us9…> Twitter<https://protect-au.mimecast.com/s/JyeYCROAWrhQK892iw7KCi?domain=combine.us9…> [Google Plus]<https://protect-au.mimecast.com/s/ach0CVAG1yhX41rGiw-pGi?domain=combine.us9…> Google Plus<https://protect-au.mimecast.com/s/e_ggCWLJ2zfxpv7JH3joiW?domain=combine.us9…> [YouTube]<https://protect-au.mimecast.com/s/1eV2CXLK3AfG63vwiJ0BLX?domain=combine.us9…> YouTube<https://protect-au.mimecast.com/s/YuQOCYWL4Bsg0PRrUpfpoV?domain=combine.us9…> [LinkedIn]<https://protect-au.mimecast.com/s/OoFzCZYM5DFxmyZJHBl42K?domain=combine.us9…> LinkedIn<https://protect-au.mimecast.com/s/htvKC1WZ5zsOjKyVi7MGp7?domain=combine.us9…> [GitHub]<https://protect-au.mimecast.com/s/PDjnC2xZ6AH6xAqMFgzUgv?domain=combine.us9…> GitHub<https://protect-au.mimecast.com/s/LQBuC3Q870Ux8V1nHKywlq?domain=combine.us9…> [RSS]<https://protect-au.mimecast.com/s/AzZOC4QZgDU6jGNXF0t9Sa?domain=combine.us9…> RSS<https://protect-au.mimecast.com/s/4TrQC5QZjEURnOmBczvtAXy?domain=combine.us…> [Email]<mailto:combine@combine.org.au> Email<mailto:combine@combine.org.au> You are receiving this email because you signed up online or at a COMBINE Australia event. unsubscribe from this list<https://protect-au.mimecast.com/s/qMJ5CxnMQNtBGK6YIqWltD?domain=combine.us9…> update subscription preferences<https://protect-au.mimecast.com/s/knClCyoNROTJjEvxTq5mtd?domain=combine.us9…> Copyright © 2018 COMBINE Australia, All rights reserved Our mailing address is: COMBINE Australia c/o Tony Papenfuss, Australian Bioinformatics and Computational Biology Society Walter and Eliza Hall Institute, 1G Royal Parade Parkville, VIC 3051 Australia Add us to your address book<https://protect-au.mimecast.com/s/TeZbC6X1k7CM3x25fppuUAa> [Email Marketing Powered by MailChimp]<https://protect-au.mimecast.com/s/f3xfCzvO0NfnPvl5TllIOS?domain=mailchimp.c…> University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

1 0

2024

2023

2022

2021

2020

2019

2018

2017

2016

bioinformatics-list September 2018